For this night in Bavaria Rooney had been asked to be a different kind of total footballer. The all-action hybrid of striker-midfielder often seen on the fields of the Premier League has Rooney as the pivotal actor, the ball either leaving or coming to him as he seeks to punch holes where it hurts the opposition.

Here he was asked to be the first defender at the tip of David Moyes's 4-5-1 formation while being ready to instantly transform into the predator who might score or create the goal that would dump Bayern out.

The blistering start Pep Guardiola's men fashioned suggested that attack-mode Rooney would indeed be feeding off scraps all evening. While Arjen Robben took up ownership of the ball in those opening moments, Rooney was operating near the centre circle or joining team-mates deeper inside United territory.

Taking up occupancy at corners – Bayern had two inside the opening five minutes – or trying to step on Toni Kroos or Philipp Lahm to snuff out the Germans' attack at birth – were his chief occupations.

This detail had been on Rooney's mind during the build-up. Of the Bayern captain, the forward said: "The most important player for me is Philipp Lahm. They've got [Franck] Ribéry, Robben and Toni Kroos who are great players but Lahm is the one who makes everything tick. He is the one you have to stop."

Yet as he settled into this role, United began to assert themselves, and Rooney was given his first gilded opportunity.

What appeared a speculative Darren Fletcher effort dropped perfectly into Rooney's path. Instant control allowed a surge towards Manuel Neuer's goal. But instead of using his left to shoot, Rooney dallied, Dante blocked him, and when Shinji Kagawa then became available the option was refused. The threat therefore fizzled out.

Guardiola had described Rooney as one of the best players he has ever seen in his career before this match. From a man who has coached Lionel Messi, Andres Iniesta and Xavi Hernández it was some compliment.

If there was a touch of exaggeration in this, there is no doubt Guardiola feared what Rooney might do as the hub of United.

An illustration came in the chance he made for Antonio Valencia's disallowed goal. Floating out to the left where Kagawa's natural inclination can also take him, Rooney played in the cross for a strike rightly chalked-off for offside.Kagawa's inclusion had been a headline selection from Moyes. At last he was handed the No10 role in a big-time game to show what he could do. The manager had been missing out by limiting him to only 13 starts – before this one – in his first season in charge.

Kagawa's four appearances for Borussia Dortmund against Bayern had all ended with the 25-year-old on the winning side. Perhaps that was a factor in Moyes's decision, and some of United's brightest moments – scant as they were due to Bayern's superb ball-retention – were created by Kagawa as he found pockets of space and plenty of team-mates as he had done so successfully for Dortmund before his £17.5m move two years ago.

Rooney, booed all night for the incident that had Bastian Schweinsteiger sent off in the first leg at Old Trafford, began the second half by taking the collector's item of a United corner.

The next corner, inevitably, was Bayern's. And, it was Rooney who rose to head the danger away as he continued to fulfil the disciplined role required by his manager.

To get to the break with Bayern not scoring had been a success, though Schweinsteiger's finish at Old Trafford meant that as the clock ticked towards the hour mark, and this game remained goalless, Bayern were probably the happier. Yet the sense grew that this had become the kind of scrappy contest that United wanted, while Bayern were struggling to find the rhythm that can often be so hypnotic.

This was confirmed when Patrice Evra let fly for a 57th-minute goal that had United ahead in the tie for the second time – and believing.

Before kick-off Moyes said: "If we can make them chase the game that will suit us because we don't want to be chasing it."

For less than two minutes the Scot had his wish. With United's players still engulfed by euphoria, Bayern swept downfield and Franck Ribéry's ball was headed home expertly by Mario Mandzukic beyond David de Gea, Evra far too slow to make the challenge.

Now, after Rooney's chance came and was messed up, first Müller then the excellent Robben showed the 28-year-old how to finish, to give Bayern a 3-1 lead on the night that meant an unassailable 4-2 advantage on aggregate and Manchester United, seventh in the Premier League, were going out of the Champions League.

That position means it will be 2015, at the earliest, that they – and Rooney – will be back in the competition.